49ers QB Smith on Crabtree: ‘He’s done the right things’

Yes, Alex Smith said, he has some chemistry issues with receiver Michael Crabtree. But the 49ers quarterback said Thursday that their struggles are limited only to the playing field and that they get along just fine.

Smith called his perceived feud with the 49ers’ No. 1 receiver: “something that has been totally off-base” after recent quotes from both player created a stir.

“Obviously, (over) the last two weeks a lot has been made of our relationship,’’ Smith said Thursday after the final day of a four-day, players-only camp. “Things have come out in the paper that I think we both wish we could take back. I know I feel that way.”

Some readers thought the remark came off as a slight – including Smith, who recoiled once he saw the quote in print.

“When I kept getting asked why he wasn’t out here, I really didn’t want to speak on his behalf. I really thought I was doing the right thing,’’ Smith said Thursday.

“Then all of a sudden I read it the next day and I was really disgusted with myself with the way it came out. It looked like a jab. I called him up and talked to him and apologized.”

Earlier this week, Crabtree questioned the widespread presumption that Smith would wind up as the 49ers starting quarterback – even though coach Jim Harbaugh has indicated for months that he expects Smith to take over that role.

Asked about the perceived slight, Smith laughed.

“I don’t want to hurt your feelings,’’ he told a reporter, “but when football players get away from football we don’t like to read all the articles during the off-season.

“I’m not even on the roster. I’m a free agent. So for him to be confused as to the quarterback situation isn’t the strangest thing in the world in my opinion. I can tell you Michael probably doesn’t read all the stuff.”

Fueling the perception of a bad vibe, Crabtree followed his controversial comments Tuesday by skipping the final three practices of so-called “Camp Alex” at San Jose State. Crabtree came to the classroom sessions but drove off as soon as teammates took the field. Crabtree told teammates he had sore feet after a bad reaction to breaking in new cleats.

On Thursday, Smith defended Crabtree’s absence by noting that the receiver once sustained a broken foot that required surgery.

“You’re talking about a guy with a foot history,” Smith said. “The last thing we wanted from this (camp) was somebody getting hurt. … Timing and things like that? We’re going to have time for that. The last thing I wanted was guys pushing their bodies to the point of an injury.”

Two other players, receiver Dominique Zeigler (knee) and rookie quarterback Colin Kaepernick (leg) were also nursing injuries and unable to practice. But they stuck around to observe and watch Smith lead the team through Harbaugh’s new playbook.

Why didn’t Crabtree stick around, too?

“This is something I really feel has been blown out of proportion,’’ Smith said. “He’s here. He wants to learn. He’s part of the team. He’s part of team functions every time we do something officially. He’s been here.

“He’s not the only guy that’s been working out alone. There are a lot of guys all over the country working out alone. It’s such a strange time. There isn’t a ‘right’ way to do things. We’re just trying to figure things out.”

On at least one count, however, Smith acknowledged a problem: on the field. The quarterback and receiver struggled to get on the same page last season, resulting in embarrassing miscommunications. Half of Smith’s 10 interceptions were on passes intended for Crabtree.

Overall, Smith had a 55.4 rating when he tried throwing the former Texas Tech star.

“He and I would both agree that we were – ‘unhappy’ would be an understatement,’’ Smith said. “There’s no question both of us are unhappy. We’d be the first to tell you that. We know we have to play better. Both of us. Absolutely. No question.”

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Smith orchestrated the four-day camp despite not being under contract with the 49ers because he expects to be back with the team. Center David Baas took a similar approach, flying out from his Florida home to participate in Thursday’s final day.

The unrestricted free agent’s was unable to make the camp’s start on Monday but made the late-week cross-country flight to show he was committed to a return.

“Really, all I can do is be a professional about it. And that’s one of the reasons I came out here – I plan on coming back,’’ Baas said. “You never know what’s going to happen with the craziness that’s going on. But I’m going to prepare like I’m coming back.”

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Kaepernick did not take the field during the camp as he continues to rehabilitate from an off-season procedure on his lower leg. Doctors have told him to take it slow.

Still, he praised Smith for doing what he can to introduce him to an NFL playbook.

“He’s been helping me with everything,’’ Kaepernick said. “He told me right at the start: If you have any questions, just ask. So anytime there’s something I don’t quite understand in the playbook, I come to him.”

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Depending on the future of the NFL lockout, the 49ers might attempt another player-only camp later this month.